It has improved since the last time I mentioned it on this list, specifically, you can now restrict the wrapping to a given selection, as in (my personal favorite):

qwrap sel "not protein" center protein

Thanks to a contribution by Giacomo Fiorin, wrapping can also be done based on VMD fragments.

Qwrap is written in C and is relatively simple-minded, hence the speed. The main limitation with respect to pbc wrap is the treatment of orthorhombic cells only - however that can change in the future.